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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 1-109921866-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=109921866&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 109921866,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_000757.6",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.416A>G",
"hgvs_p": "p.Tyr139Cys",
"transcript": "NM_000757.6",
"protein_id": "NP_000748.4",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 554,
"cds_start": 416,
"cds_end": null,
"cds_length": 1665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000329608.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000757.6"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.416A>G",
"hgvs_p": "p.Tyr139Cys",
"transcript": "ENST00000329608.11",
"protein_id": "ENSP00000327513.6",
"transcript_support_level": 1,
"aa_start": 139,
"aa_end": null,
"aa_length": 554,
"cds_start": 416,
"cds_end": null,
"cds_length": 1665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000757.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000329608.11"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.416A>G",
"hgvs_p": "p.Tyr139Cys",
"transcript": "ENST00000369802.7",
"protein_id": "ENSP00000358817.3",
"transcript_support_level": 1,
"aa_start": 139,
"aa_end": null,
"aa_length": 554,
"cds_start": 416,
"cds_end": null,
"cds_length": 1665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000369802.7"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.416A>G",
"hgvs_p": "p.Tyr139Cys",
"transcript": "ENST00000369801.1",
"protein_id": "ENSP00000358816.1",
"transcript_support_level": 1,
"aa_start": 139,
"aa_end": null,
"aa_length": 438,
"cds_start": 416,
"cds_end": null,
"cds_length": 1317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000369801.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.476A>G",
"hgvs_p": "p.Tyr159Cys",
"transcript": "ENST00000875283.1",
"protein_id": "ENSP00000545342.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 574,
"cds_start": 476,
"cds_end": null,
"cds_length": 1725,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875283.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.476A>G",
"hgvs_p": "p.Tyr159Cys",
"transcript": "ENST00000875286.1",
"protein_id": "ENSP00000545345.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 574,
"cds_start": 476,
"cds_end": null,
"cds_length": 1725,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875286.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.416A>G",
"hgvs_p": "p.Tyr139Cys",
"transcript": "NM_172212.3",
"protein_id": "NP_757351.2",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 554,
"cds_start": 416,
"cds_end": null,
"cds_length": 1665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_172212.3"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.416A>G",
"hgvs_p": "p.Tyr139Cys",
"transcript": "ENST00000875284.1",
"protein_id": "ENSP00000545343.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 554,
"cds_start": 416,
"cds_end": null,
"cds_length": 1665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875284.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.230A>G",
"hgvs_p": "p.Tyr77Cys",
"transcript": "ENST00000875282.1",
"protein_id": "ENSP00000545341.1",
"transcript_support_level": null,
"aa_start": 77,
"aa_end": null,
"aa_length": 492,
"cds_start": 230,
"cds_end": null,
"cds_length": 1479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875282.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.230A>G",
"hgvs_p": "p.Tyr77Cys",
"transcript": "ENST00000875287.1",
"protein_id": "ENSP00000545346.1",
"transcript_support_level": null,
"aa_start": 77,
"aa_end": null,
"aa_length": 492,
"cds_start": 230,
"cds_end": null,
"cds_length": 1479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875287.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.416A>G",
"hgvs_p": "p.Tyr139Cys",
"transcript": "NM_172210.3",
"protein_id": "NP_757349.2",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 438,
"cds_start": 416,
"cds_end": null,
"cds_length": 1317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_172210.3"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.293A>G",
"hgvs_p": "p.Tyr98Cys",
"transcript": "ENST00000488198.5",
"protein_id": "ENSP00000433837.1",
"transcript_support_level": 3,
"aa_start": 98,
"aa_end": null,
"aa_length": 284,
"cds_start": 293,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000488198.5"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.416A>G",
"hgvs_p": "p.Tyr139Cys",
"transcript": "NM_172211.4",
"protein_id": "NP_757350.2",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 256,
"cds_start": 416,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_172211.4"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.416A>G",
"hgvs_p": "p.Tyr139Cys",
"transcript": "ENST00000420111.6",
"protein_id": "ENSP00000407317.2",
"transcript_support_level": 5,
"aa_start": 139,
"aa_end": null,
"aa_length": 256,
"cds_start": 416,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000420111.6"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.293A>G",
"hgvs_p": "p.Tyr98Cys",
"transcript": "ENST00000958976.1",
"protein_id": "ENSP00000629035.1",
"transcript_support_level": null,
"aa_start": 98,
"aa_end": null,
"aa_length": 215,
"cds_start": 293,
"cds_end": null,
"cds_length": 648,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958976.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.230A>G",
"hgvs_p": "p.Tyr77Cys",
"transcript": "ENST00000875285.1",
"protein_id": "ENSP00000545344.1",
"transcript_support_level": null,
"aa_start": 77,
"aa_end": null,
"aa_length": 194,
"cds_start": 230,
"cds_end": null,
"cds_length": 585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875285.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.230A>G",
"hgvs_p": "p.Tyr77Cys",
"transcript": "ENST00000913371.1",
"protein_id": "ENSP00000583430.1",
"transcript_support_level": null,
"aa_start": 77,
"aa_end": null,
"aa_length": 194,
"cds_start": 230,
"cds_end": null,
"cds_length": 585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913371.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.437A>G",
"hgvs_p": "p.Tyr146Cys",
"transcript": "ENST00000527192.5",
"protein_id": "ENSP00000434527.1",
"transcript_support_level": 4,
"aa_start": 146,
"aa_end": null,
"aa_length": 149,
"cds_start": 437,
"cds_end": null,
"cds_length": 451,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000527192.5"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.293A>G",
"hgvs_p": "p.Tyr98Cys",
"transcript": "ENST00000525659.5",
"protein_id": "ENSP00000431547.1",
"transcript_support_level": 4,
"aa_start": 98,
"aa_end": null,
"aa_length": 112,
"cds_start": 293,
"cds_end": null,
"cds_length": 340,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000525659.5"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.293A>G",
"hgvs_p": "p.Tyr98Cys",
"transcript": "XM_017000369.1",
"protein_id": "XP_016855858.1",
"transcript_support_level": null,
"aa_start": 98,
"aa_end": null,
"aa_length": 513,
"cds_start": 293,
"cds_end": null,
"cds_length": 1542,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000369.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.416A>G",
"hgvs_p": "p.Tyr139Cys",
"transcript": "XM_047446752.1",
"protein_id": "XP_047302708.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 256,
"cds_start": 416,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047446752.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "n.231A>G",
"hgvs_p": null,
"transcript": "ENST00000526001.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000526001.1"
}
],
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"dbsnp": null,
"frequency_reference_population": 0.0000027616834,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000276168,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1765533983707428,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.068,
"revel_prediction": "Benign",
"alphamissense_score": 0.2469,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.138,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000757.6",
"gene_symbol": "CSF1",
"hgnc_id": 2432,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.416A>G",
"hgvs_p": "p.Tyr139Cys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}